Shinobi of the Reaper War
by DfangOO
Summary: After Naruto's battle with Pain he wakes up 14 years later in a Cerberus facility. He must now join Shepard and her crew to stop the Reapers before everything is lost.
1. Chapter 1

**Disclaimer: **I do not own Naruto or Mass Effect. I claim no rights to these properties or anything related.

**Chapter 1**

A 30-year-old man with blonde hair and whisker marks on his cheeks is waking up to the sound of alarms. The noise was loud and mixed with the sounds of chaos outside his room. He looks around at where he is, taking in his surroundings. Noticing his orange and black jumpsuit in the corner he gets off the bed and puts on his clothes.

"You, you're awake," came a voice over a speaker.

"Who and where are you," the blonde man asked.

"There's no time, this facility is under attack by mechs. There's a pistol on the table next to you; grab it and get out of there. I'll guide you along the way."

Not seeing any other options the blonde looks at the table to see only one object lying on top of it. He grabs it and heads out the door. After making his way through the halls he sees a couple of people shooting some machines from behind cover. Looking over toward the door they notice him too. "What they hell, you're awake too," said an African American man.

"Who's this Jacob," asked a red headed woman.

"In a minute Shepard, let's finishing these things off first," replied the man. The blonde then joins them behind cover. "You know how to use that thing," Jacob asked the blonde.

"I don't even know what this thing is," he answered.

"Great, just stay down and let us handle this," said Jacob.

"How about you just let me do this," said the blonde before doing something with his hands. "SHADOW CLONE JUTSU," he called out as multiple copies of the blonde appeared and took out the mechs across from them. To say that the other two were shocked and impressed would be putting it mildly.

"That was impressive," said the red headed woman looking the blonde over. She couldn't help but notice how attractive he was. "My name is Commander Shepard, who are you?"

"My name's Naruto Uzumaki," he replied while looking her over as well. He had to admit to himself that she was attractive. "Who are you guys and what's going on here?"

"I'm Jacob Taylor, how did you do what you just did," he asked the blonde.

"I think we can worry about that later. We need to get out of here first and then we can play 20 questions," said Shepard.

"Sorry, I just had to ask. You're right though; we really should get out of here. The shuttles are through this way," Jacob said heading toward the door.

"Naruto, you're not wearing any armor so watch yourself," said Shepard. She gave him a brief demonstration on how to use his pistol before they were off.

They ended up in a room where Wilson was down with an injured leg. "Wilson, are you alright," Jacob asked.

"My leg has been shot, no I'm not alright. Wait, they're both awake," Wilson looked at Jacob for answers. Jacob just nodded before Wilson continued, "There's some Medi-gel over on the wall. It should fix my leg."

After Shepard retrieved the Medi-gel and fixed Wilson's leg Jacob addressed Shepard, "I think it's time you know who we work for Shepard. Project Lazarus that rebuilt you, this facility all belong to Cerberus."

"I remember coming up against Cerberus while I was hunting down Seran," Shepard said.

"Who is Cerberus," asked Naruto.

"They're a pro human extremist group. They've crossed the line countless times in the name of humanity," Shepard told him. "I don't care what Cerberus wants. I'll never join them."

"Is there really time for this? We need to get moving," said Wilson.

"We need to find Miranda," said Shepard.

"Miranda, she's probably dead already. Even if she isn't we can't trust her. She's probably behind all this," said Wilson.

"If she was behind this why has she been helping me," asked Shepard. "She might be able to tell us more once we find her."

"I for one am sick of sticking around here. Talking about this all day isn't getting us there any faster," said Naruto.

"Alright let's move," ordered the Commander.

After fighting their way to the shuttles they ran into Miranda. Upon opening the door she shot Wilson. "What the hell, why did you do that," Naruto exclaimed.

"Wilson betrayed us, he's the one that caused these mechs to attacks in the first place," Miranda explained.

"Guess I'll take your word on that. I know you work for Cerberus," said Shepard.

"Jacob, feeling chatty were we?"

"Keeping this from the Commander isn't the best way to win her over," said Jacob.

"Well if there's nothing else let's get into the shuttle. The Illusive Man wants to meet with both of you," Miranda said looking at Shepard and Naruto.

They boarded the shuttle and took off from the facility. Naruto went wide-eyed once he looked out the window into the empty void of space. "Where are we," he asked.

"I take it you've never been in space before," Shepard asked the blonde to her right.

"What do you remember before waking up back there," Miranda asked the blonde.

"It's all coming back to me now. The last thing I remember I was fighting Pain. I just managed to beat him before I blacked out. Next thing I know I'm waking up back there," Naruto explained.

"How long was I out and how did I end up there," Naruto asked.

"Cerberus found you after tracking Geth activity to an uncharted world. A team went in to take investigate and found you alone and unconscious. You were brought back to our facility and remained in some kind coma," Miranda explained.

"What, why didn't you take me to a nearby village or something? Why did you bring me there," Naruto exclaimed.

"We had orders, you were from an unknown world and the Illusive Man wanted you brought back for examination. He wanted to learn more about you and the world you come from," said Miranda.

"Well then I'll just have to have a word with this Illusive Man when we get there," said Naruto not looking happy.

"The Illusive Man is very powerful, you might want to be careful how you speak to him," Miranda warned.

"I don't give a damn if he's the Hokage of the known universe. I don't appreciate being taking against my will," said Naruto.

Shepard couldn't help but smile at the blonde. 'I think I could get to like this guy,' she thought to herself. "Don't worry, we'll both get answers once we see him."

Naruto looked over and blushed when she smiled at him. Something about those green eyes and that smile made his heart rate increase. Shepard didn't fail to notice his blush. "Yeah I guess you're right, anyway you never told me how long I was out," Naruto said looking back at Miranda.

"We found you in that coma 14 years ago," Miranda told him.

"WHAT, I'VE BEEN IN A COMA FOR 14 YEARS," Naruto couldn't believe what he was hearing.

"I'm afraid so, we didn't know when or if you would wake up," Jacob chimed in.

"That means I'm like 30 now. I can't believe I just missed 14 years of my life," said Naruto. Shepard put a reassuring hand on Naruto's shoulder.

"What about me, how long have I been out," Shepard asked.

"It's been 2 years since the attack on the Normandy," said Jacob.

"I've been gone for 2 years. How did I end up at a Cerberus facility," the Commander asked.

"After we recovered your body we began reconstructing you. The Illusive Man wanted you brought back just the way you were," Miranda explained.

"I need to ask you a few questions to make sure your memory is intact Shepard. On Virmire you left one of your team behind to die when you destroyed Seran's cloning facility," said Miranda.

"Lieutenant Kaiden Alenko, we tried to save as many lives as we could. There was no time to save Ash and Kaiden both so I had to make a choice. I chose to save Ashley and lost a friend that day," Shepard said regretfully. It was Naruto's turn to put a reassuring hand on her shoulder for which Shepard was grateful.

"After Seran's attack on the Citadel humanity was offered a spot on the council. Who did you recommend," Miranda asked.

"I recommended Captain Anderson, I felt that he would be a better choice over Udina."

"Isn't that enough Miranda," Jacob asked.

"I suppose so, we're nearing our destination anyway," she told them.

Once they docked the group exited the shuttle and made their way in. Miranda directed Naruto and Shepard to where they would be meeting the Illusive Man.

"Commander Shepard and our comatose friend," said the Illusive Man.

"I thought we'd be meeting face to face," Shepard stated.

"I have my reasons for meeting this way. I understand you displayed some impressive abilities back there," the shadowy figure said to Naruto.

"Where the hell do you get off taking me off my own world? You even kept me here for 14 years, who the hell to you think you are," said an upset Naruto.

"The world you come form is unknown to us. We only found it while tracking some Geth activity. I was hoping we could learn more from talking to you but you never woke up until now," he answered.

"You should have taken me to a village or something. You had no right to keep me here all this time," said the blonde.

"You may not like what we did but we spent all this time trying to figure out a way to wake you from your coma."

"Why did you have me brought back Illusive Man? What do you want," Shepard asked.

"I want your help Shepard, we both know there's a threat out there bigger than anything we've ever seen," said the Illusive Man.

"The Reapers," she simply said.

"Correct, no one else understands the gravity of the situation. One of our colonies, Freedom's Progress has been attacked. Colonists are missing and I would like you to investigate," said the Illusive Man.

"I don't trust you Illusive Man, but if you're right then more human colonies could be next," Shepard said.

"Which is why we need to know what's going on. After what happened back there out blonde friend here might be a big help to you," said the Illusive Man.

"Give me one good reason why I should do anything for you," said Naruto.

"You don't know this but there's a threat out there bigger than you can imagine. These Reapers could wipe out all life in the galaxy if we don't stop them. Your home planet would also be wiped out along with everyone you know," he explained to Naruto.

"You're kidding, there's something out there that powerful and dangerous," he said in disbelief.

"Just ask Shepard, she knows as well as I do the danger this threat poses," Illusive Man said.

"It's true, every species and every planet is at stake here," Shepard confirmed.

"I guess it couldn't hurt to take a look and see what we find," Naruto finally said.

"Then it seems we're in agreement. Shepard, you should get him some armor and weapons," Illusive Man finished before the conversation ended.

"I never thanked you for the help back there. I know this all must be new for you but I could really use all the help I can get," Shepard said to the blonde now that they were alone.

"Don't mention it, I'm always happy to help. If this threat is really as bad as you say it is we could lose everything," he said.

"Yes we could, but if I can help it we won't. I'm dedicated to fighting this thing but I can't do it alone," Shepard admitted.

"You won't have to, I'll do whatever I can to help stop this," Naruto said with a smile.

"Thanks, now let's go get you suited up," Shepard said before starting to walk off.

"Wait, what's you first name? I mean it's not Commander is it," Naruto asked.

Shepard laughed and replied, "It's Jane, Jane Shepard." Naruto smiled and followed her up to prepare to depart.


	2. Chapter 2

**Disclaimer: **I do not own Naruto or Mass Effect. I claim no rights to these properties or anything related.

**Chapter 2**

The shuttle landed at Freedom's Progress and the group exited. It was eerily quiet with no sign of life. "Well this isn't creepy at all," Naruto commented.

"How's the armor," Shepard asked him.

"Well it's going to take some getting used to. My movements are more restricted than normal," the blonde told her.

"Let's start searching the area," Shepard ordered.

On the way they encountered hostile mechs. After dealing with them the group came to a building to find a group of Quarians. They raised their guns at the newcomers on sight when a familiar face to Shepard stepped it. "Everyone put your weapons down. Shepard, you're alive?"

"Tali, I'm surprised to see you here," Shepard said.

"I'm surprised to see you since I thought you were dead," Tali said.

"I was in some kind of coma for 2 years while Cerberus rebuilt me," Shepard told her.

"Does this mean you've joined Cerberus now," asked the Quarian.

"I haven't joined Cerberus, they asked me to investigate what happened here. Do you know what happened here," Shepard asked.

"A Quarian, Veetor was here on pilgrimage. If anyone knows what happened it would be him. He fled into a warehouse and activated the mechs," Tali said.

"Sounds like we need to find this Veetor then," Naruto said.

"Are we really considering working with Cerberus," Prazza asked.

"No we're working with Shepard, if that's a problem go wait on the ship," Tali said. Prazza made no further comment.

"We should split up into two teams. We'll cover more ground," suggested Shepard.

"Agreed, we'll stay in radio contact. It's good to have you back Shepard," were Tali's last words before they split up.

"Friend of yours," asked Naruto.

"Her name's Tali and yes. She helped me stop Saren 2 years ago," Shepard told him. "Once we're done here I'll have to make it a point to get you caught up on what's going on. You're still having trouble with those guns aren't you?"

"I don't have a clue how to use these things. I'm fine relying on my jutsu for now," the blonde told her.

"I'd still like to know what that is and how you do it," Jacob said.

"I admit I'm curious myself. I've never seen anything like it," said Shepard.

"I'll tell you all about it once we have some free time," Naruto said. Shepard just nodded and smiled at him.

They made their way further into the colony while fighting off more mechs. While they continued to move forward Tali's voice came over the radio. "Shepard, Prazza and his men went on ahead. They want to get to Veetor before you. I told them to wait, but they wouldn't listen."

"Damn, I knew they would betray us. We should have never trusted them," Miranda said.

When they finally reached Prazza and his men they were being torn apart by a Heavy Mech. Shepard and her group ducked behind cover. It continued to fire at them while moving forward.

"I've got an idea just give me some cover," Naruto said.

"What are you planning," Shepard asked.

"Trust me this will work," Naruto said looking at her.

"Alright then we'll cover you. Just don't do anything reckless," Shepard said. Naruto just winked at Shepard and quickly disappeared. 'He moves fast,' she quickly thought to herself before firing at the Heavy Mech.

Naruto reappeared above the Heavy Mech with a blue orb in hand. He slammed it into the machine, driving it into the ground. "RASENGAN," he called out before the mech exploded.

"NARUTO," Shepard called out worried. The mech was destroyed, but she feared the worst for her new friend. Naruto's body that was lying on the ground vanished in a puff of smoke. The real Naruto walked out unharmed. Shepard walked over the Naruto and got in his face. "Don't you ever worry me like that again! What the hell was that?"

"I didn't know what would happen once I hit that thing with my Rasengan. So I sent a clone to do it for me and test it out," Naruto explained.

"Next time you want to try some shit like that let me know. I thought you just got yourself killed you know that," Shepard said.

"Look I'm sorry I had you worried," said Naruto apologetically.

"A little heads up next time would be nice," she said. "Now, let's get in there and see what Veetor can tell us."

They entered to find Veetor staring intently at large monitors. Veetor turns to the team and is surprised to see humans. "You're humans, why didn't they take you too?"

"Why didn't who take us? Did you see what happened to these people," Naruto asked.

"The monsters came and took everyone," Veetor said before activating the monitors to show them what happened.

"What the hell are those things," Naruto asked referring to the bug like people on the screen.

"Those are Collectors aren't they," Jacob asked.

"Yeah they are," said Miranda.

It was then that Tali walked in to meet the group. "Shepard, I need to get Veetor out of here so he can receive medical attention."

"Wait, this Quarian has information that we need, we have to take him with us," Miranda said to Shepard.

"You can take Veetor's Omni-Tool data," Tali said.

"Veetor will go with Tali and we'll take his Omni-Tool data. They should be enough," Shepard said. "You know Tali we could use your help."

"I can't Shepard, I have my own business to take care of and I need to get Veetor out of here," said the Quarian.

"Well stay safe ok Tali. Maybe we'll see each other again," Shepard said.

"Right, thanks for everything Shepard," Tali said before leaving with Veetor.

After they had left Shepard and Naruto met with the Illusive Man again. "I trust you found what we were looking for," he said.

"The Collectors are abducting humans. Just don't know why," Shepard said.

"Whatever these things are they need to be stopped. Before anymore people get taken," said Naruto.

"I take it you're on board then," asked the Illusive Man.

"Yes, these things need to be stopped. That still doesn't mean I trust you," said the blonde.

"I'm with him, we can't let anymore colonies get hit. I still don't trust you either," said Shepard.

"Very well, I have something for you will help you in your mission. A ship waiting for you and an old friend of yours," said the Illusive Man. The conversation ended and through the door walked Joker.

"Joker, is that you? I'm surprised to see you here," said Shepard.

"Right back at you, I remember you ending up in space after the Normandy was attacked. Guess even death couldn't stop you," said Joker.

"Cerberus rebuilt me for 2 years. I'm surprised to see you with them," Shepard commented.

"After the attack the Alliance grounded me. Cerberus were the only ones that would let me fly," Joker said. "Who's the new guy?"

"His name's Naruto and he's been helping me," Shepard said. "Naruto this is Joker, he was the pilot for the Normandy when I tracked down Saren."

"Speaking of the Normandy there's something I want to show you," said Joker. The three of them walked through the halls until they came to see a ship through a window.

"That's big," said Naruto.

"She's beautiful isn't she? What do you think Commaner," asked Joker.

"I think it's just the right ship," said Shepard.

After taking off Naruto was down on Deck 3. Once they got going Shepard came down to talk to him. "Are you getting settled in alright," she asked.

"Yeah, this is so different from what I'm used to. So what brings you down here," he asked.

"I believe you mentioned an explanation before," she said.

"I guess I did didn't I? Alright, you might want to sit down," Naruto said as Shepard sat down on the couch. "What do you want to know first?"

"How about how that jutsu of yours works," Shepard said.

"Well, where I come from we use what's called chakra. Chakra is the combination of physical and spiritual energy. By channeling this energy we can perform jutsu," Naruto explained.

"Can everyone on your home planet do this," she asked.

"Not everyone, using chakra and learning jutsu takes training. I attended a Ninja Academy when I was little and became a ninja when I was 12. I learned how to use chakra in the academy," he told her. Naruto went on to explain about being a ninja and what they do.

"I see, you said you were fighting someone before you went into that coma. What was that about," Shepard asked.

"That's tied to a subject I'd rather not get into right now. It has a lot to do with me so do you mind if we save this for another time," Naruto asked.

"Of course, I want all my crew to feel like they can talk to me. When you're ready to talk about it I'll be ready to listen," Jane told him.

"Thanks Shepard, it's just not easy for me to talk about. Just give me a little time," Naruto said. "Can I ask you something now?"

"Of course, ask me anything you like and when it's just us you can call me Jane," she told him.

"Do you ask all your crew questions like this," he asked.

"I like to get to know all my crew. We're all in this together so we should know one another," she said.

"That makes since, I thought it might just be a personal interest in me," the blonde said.

"Who says it's not," Shepard said with a smirk. "I like you Naruto and I'd like to get to know more about you."

Naruto blushed at hearing that. "You might not like what you learn," he said a little sad.

"What makes you say that," Jane asked.

Naruto just sighed and replied, "It all goes back to something that happened the day I was born. Because of that I've experienced a lot of pain in my life."

"I'm sorry, whatever it is I doubt it'll make me think less of you. If you need more time there's no rush," Shepard said. Naruto smiles as Jane got up to leave. "I should be getting back to up there. We'll be landing at the Citadel soon, I'm going to meet with Captain Anderson."

"That's that guy you suggested for councilor right," Naruto asked.

"Yes that's right, I need to meet with him and the rest of the council. I'm also sending down some datapads for you to read. It'll get you caught up and what's going on in the galaxy and our current situation."

"What's a datapad," Naruto asked.

Shepard smiled and said, "I'll have Kelly show you what they are and how they work when she brings them to you." Naruto nodded and Shepard walked out the door.


End file.
